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Ten computational modelling cases were studied to determine the vulnerability of the Lagoon System of Jacarepaguá-Brazil to the impact of different combinations of storm surges, sea level rise, heavy rainfall, and dredging bathymetry. The analysis included maximum water elevations and their time of occurrence, and tidal prism. The main results show that storm surge has the most impact on the maximum water elevations, overcoming the impact of an increase in the sea level, river flow and changes in bathymetry. The planned dredging project and higher storm surges would improve water renovation in the lagoons, due to a higher tidal prism.